On Thu, Sep 30, 2010, Francesco Pietra wrote:
> Incorrect handling of phenylalanine amide by antechamber 1.2 in amber
> 10 (or mishandling of antechamber by the operator).
>
> Phenylalanine amide triprotonated at N, thus charge +1. The structure
> is correct in both Chimera and VMD.
>
> $AMBERHOME/exe/antechamber -i pha.NH3.pdb -fi pdb -o pha.prepin -fo
> prepi -c bcc -s 2 -nc +1
>
> $AMBERHOME/exe/parmchk -i pha.prepin -f prepi -o pha.frcmod
>
> These prepin and frcmod file are not accepted by Chimera, while VMD
> shows a highly deformed structure (much too long C=O bond, phenyl
> hydrogens out of plane and ring distorted; NH3 also distorted.
>
> Thanks for indicating my mistakes in the antechamber input files.
Can you post the input pdb file so we can look at this? There may be a
problem in converting to internal coodinates. As a check, try creating a mol2
file rather than a prepin file: the output coordinates should be the same as
the input ones.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 30 2010 - 04:30:05 PDT
